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gyacomo/matlab/plot/plot_fa_gene.m
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plot_fa_gene.m
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function plot_fa_gene(OPTIONS)
folder = OPTIONS.folder;
TIMES = OPTIONS.times;
specie = OPTIONS.specie;
PLT_FCT= OPTIONS.PLT_FCT;
file = 'coord.dat.h5';
vp = h5read([folder,file],'/coord/vp'); nvp = numel(vp);
mu = h5read([folder,file],'/coord/mu'); nmu = numel(mu);
z = h5read([folder,file],'/coord/z');
[XX,SS] = meshgrid(mu,vp);
switch OPTIONS.iz
case 'avg'
zcomp_name = ' z-avg';
zcomp = @(x) squeeze(mean(x,1));
otherwise
zcomp_name = [' z=',sprintf('%2.2f',z(OPTIONS.iz))];
zcomp = @(x) squeeze(x(OPTIONS.iz,:,:));
end
[~,iv0] = min(abs(vp));
[~,im0] = min(abs(mu));
file = 'vsp.dat.h5';
time = h5read([folder,file],'/vsp/time');
fig = figure;
G_t = [];
Gdata = 0;
for T = TIMES
[~, it] = min(abs(time-T));
tmp = h5read([folder,file],['/vsp/',OPTIONS.FIELD,'/',sprintf('%10.10d',it-1)]);
Gdata = Gdata + tmp;
G_t = [G_t time(it)];
end
Gdata = Gdata ./ numel(TIMES);
if OPTIONS.ONED
switch specie
case 'e'
FFa = zcomp(Gdata(:,:,:,2));
FFa = abs(FFa)./max(max(abs(FFa)));
subplot(1,2,1)
plot(vp,FFa(:,im0)); hold on;
subplot(1,2,2)
plot(mu,FFa(iv0,:)); hold on;
case 'i'
FFa = zcomp(Gdata(:,:,:,1));
FFa = abs(FFa)./max(max(abs(FFa)));
end
subplot(1,2,1)
plot(vp,FFa(:,im0)); hold on;
legend(specie)
xlabel('$v_\parallel, (\mu=0)$'); ylabel('$\langle |f_a|^2\rangle_{xy}^{1/2}$');
subplot(1,2,2)
plot(mu,FFa(iv0,:)); hold on;
legend(specie)
xlabel('$\mu, (v_\parallel=0)$'); ylabel('$\langle |f_a|^2\rangle_{xy}^{1/2}$');
else
switch specie
case 'e'
name = '$f_e(v_\parallel,\mu_p)$';
FFa = zcomp(squeeze(Gdata(:,:,:,2)));
FFa = abs(FFa)./max(max(abs(FFa)));
switch PLT_FCT
case 'contour'
contour(SS,XX,FFa);
case 'contourf'
pclr = contourf(SS,XX,FFa);
case 'pcolor'
pclr = pcolor(SS,XX,FFa); set(pclr, 'edgecolor','none'); shading interp
end
case 'i'
name = '$f_i(v_\parallel,\mu_p)$';
FFa = zcomp(squeeze(Gdata(:,:,:,1)));
FFa = abs(FFa)./max(max(abs(FFa)));
switch PLT_FCT
case 'contour'
contour(SS,XX,FFa,(nvp+nmu)/2);
case 'contourf'
pclr = contourf(SS,XX,FFa,(nvp+nmu)/2);
case 'pcolor'
pclr = pcolor(SS,XX,FFa); set(pclr, 'edgecolor','none'); shading interp
end
end
if numel(TIMES) == 1
title(['Gene ',name,zcomp_name,', $t = ',sprintf('%2.2f',time(it)),'$']);
else
title(['Gene ',name,zcomp_name,', averaged $t\in$[',sprintf('%2.2f',G_t(1)),',',sprintf('%2.2f',G_t(end)),']']);
end
clear FFi FFe tmp Gdata
end
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